Alignment represention:
-> The line labled 'iso' is the isostericity base-pair indication. A Star '*' represents the matched location in the seqeunce is a of part a matched isosteric base-pair.A plus symbol '+' represents the matched location is a part of matched non-isosteric base-pair.
-> The line labeled 'edge' is the interacting edges. 'W' is for Watson-Crick, 'H' is for Hoogsteen, and 'S' is for sugar edge.Upper case letters are for 'cis' orientation base-pairs while lower case letters are for 'trans' orientation base-pairs.
-> The line labeled 'struc' represents the base-pair locations. A pair of '(' and ')' represent the base-pair that was identified in the first stage,while '<' and '>' represent the base-pair that was identified in the second stage.
-> A dot in the sequence represents the breakage location of the original sequence due to presentation of multiple strands in the query motif.An '-' symbol represents a gap in the sequence.
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


Alignment Score: 28.200


Aligning:
Query:	3U5H_5:2930-2936_2886-2892_2909-2916
Target:	1S72_0:2596-2602_2552-2555_2580-2582

iso	....*................*..
edge	....s................s..
struc	....(................)..

iso	..*.*...................
edge	..s.h...................
struc	..(.)...................

	ACUAAUA.UAUCAUA.UAAGCGUU
	| *|*  . | ||| .    |*| 
	AUUAA--.-AGCAU-.----CGUG

struc	..(.)...................
edge	..s.h...................
iso	..*.*...................

struc	....(................)..
edge	....s................s..
iso	....*................*..



Alignment Score: 28.200


Aligning:
Query:	3U5H_5:2930-2936_2886-2892_2909-2916
Target:	3J7Y_A:3048-3054_3004-3007_3032-3034

iso	....*................*..
edge	....s................s..
struc	....(................)..

iso	..*.*...................
edge	..s.h...................
struc	..(.)...................

	ACUAAUA.UAUCAUA.UAAGCGUU
	| *|*  . | ||| .    |*||
	AUUAA--.-AGCAU-.----CGUU

struc	..(.)...................
edge	..s.h...................
iso	..*.*...................

struc	....(................)..
edge	....s................s..
iso	....*................*..



Alignment Score: 25.600


Aligning:
Query:	3U5H_5:2930-2936_2886-2892_2909-2916
Target:	4A1B_1:2918-2924_2874-2877_2902-2904

iso	....*................*..
edge	....s................s..
struc	....(................)..

iso	..*.*...................
edge	..s.h...................
struc	..(.)...................

	ACUAAUA.UAUCAUA.UAAGCGUU
	 |*|*||.||||   .     *| 
	GCUAAUA.UAUC---.-----GUC

struc	..(.)...................
edge	..s.h...................
iso	..*.*...................

struc	....(................)..
edge	....s................s..
iso	....*................*..



Alignment Score: 28.200


Aligning:
Query:	3U5H_5:2930-2936_2886-2892_2909-2916
Target:	4QCN_A:2573-2579_2529-2532_2557-2559

iso	....*................*..
edge	....s................s..
struc	....(................)..

iso	..*.*...................
edge	..s.h...................
struc	..(.)...................

	ACUAAUA.UAUCAUA.UAAGCGUU
	| *|*  . | ||| .    |*||
	AUUAA--.-AGCAU-.----CGUU

struc	..(.)...................
edge	..s.h...................
iso	..*.*...................

struc	....(................)..
edge	....s................s..
iso	....*................*..



Alignment Score: 28.200


Aligning:
Query:	3U5H_5:2930-2936_2886-2892_2909-2916
Target:	2QBG_B:2561-2567_2517-2520_2545-2547

iso	....*................*..
edge	....s................s..
struc	....(................)..

iso	..*.*...................
edge	..s.h...................
struc	..(.)...................

	ACUAAUA.UAUCAUA.UAAGCGUU
	  *|*  . | ||| .    |*| 
	UUUAA--.-AGCAU-.----CGUA

struc	..(.)...................
edge	..s.h...................
iso	..*.*...................

struc	....(................)..
edge	....s................s..
iso	....*................*..



Alignment Score: 29.400


Aligning:
Query:	3U5H_5:2930-2936_2886-2892_2909-2916
Target:	1VX6_A:3289-3295_3245-3248_3273-3275

iso	.**.***...............*.
edge	.ws.hwH...............W.
struc	.((.))(...............).

	ACUAAUA.UAUCAUA.UAAGCGUU
	 **|***.||||   .     |* 
	GCUAAUA.UAUC---.-----GUC

struc	.((.))(...............).
edge	.ws.hwH...............W.
iso	.**.***...............*.